A runny filing in a pecan pie would be caused by either the incorrect ingredients, incorrect amounts of ingredients or insufficient baking time.
My pecan pie recipe includes three eggs, salt, sugar, butter, corn syrup and vanilla (and pecans, of course). It bakes at 350 F. for an hour to cook the sugars to thicken them and to cook the eggs which also act as a thickener.
When you have a chance, post your recipe or just compare it to this one or others and compare the ingredients and cooking times.
"If you want to make an apple pie from scratch, you must first create the universe." -Carl Sagan